During the second phase, we use BSHMM for a more exploratory purpose. We want to investigate the methylation patterns of P. Tricornutum in a way similar to the analyses in \cite{Huff_2014} of other diatoms. The available datasets for P. Tricornutum are shown in figure. \ref{fig:igv}. There are two distinct characteristics we want to explore. First we analyze every highly methylated region and look for any repetitive pattern similar to other organisms, independently for any other data. The second objective is to explore the correlation between the methylation profile and snRNA expression levels.

But before getting into the analysis of P. Tricornutum, we want to make sure our methods are reliable by trying to replicate some of the results exposed in \cite{Huff_2014}.